The Pokémon anime will always be how the series is most known, for better or worse. Pokemon will always speak Pokémon Speak, Team Rocket will always be humorous, and it'll always be considerably more toned down than the games. Certain characters can't quite break the rep of their anime counterparts.
Because of 4Kids Entertainment and their infamous macekres, anime dubs are almost always disliked by a subset of anime fans no matter how accurate they are to the original version* Cowboy Bebop would be the agreed-upon exception to this rule, thus causing the neverending Subbing versus Dubbing wars that have torn North American anime fandom apart.
For a concrete example, the 4Kids dub of One Piece has probably kept many anime fans away from the series, since they believe it's a childish series with no serious story to it. It's not just about a kid made of rubber wanting to become King of the Pirates and having to face bad guys armed with "poison suction cups" or brightly-colored "pop-guns". It also hasn't even been owned by 4Kids since early 2007. However, the ink stain may be lifting. Since Funimation bought the rights, uncut DVD releases have been big sellers on Amazon's anime section; and when the uncut version was added to the revived Toonami block in 2013, it regularly garnered some of the highest ratings of the evening, along with Bleach and Naruto.
Perhaps a mild version, but many people only know Dragon Ball Z for its anime adaptation. This causes people to stereotype it as having whole episodes of powering up, pointless filler, and many an Inaction Sequence, whereas the manga had none of these. Still, Dragon Ball Z is a very popular anime, so it's not all bad.
Shōnen Anime such as Naruto have become a version of this to non-fans of anime. Despite the medium encompassing multiple genres, with many having extremely fluid animation and mature story lines, the popularity of the mainstream Shonen anime as led many detractors to view anime as being filled with cliches, low-budget, filler-packed, and poorly animated.
Indecisively the case with Sailor Moon. Some argue the DiC-produced dub of the anime that ran in North America is a more offensive Macekre than anything 4Kids ever did. Nonetheless it still earned the series a large number of fans of both sexes, and had enough staying power that 15 years later, the uncut release of the original manga shot to the top of the graphic novel sales charts (often coming in second only to Batman).
The movie adaptation of Tank Girl, which many critics saw as the comic's swansong (and which pissed off the original creator so badly that he didn't write the character again for a decade). Members of its cult following might disagree, though.
The first sound version of Frankenstein simplified and compressed the story considerably and changed the character of Frankenstein's creation. In particular, the monster in the original story was actually about as lithe as a human, could speak, and was very intelligent, not the stiff, shambling, groaning monster of the movies. He also did not have bolts in his neck or a cylindrical flat-top head. The movie solidified the idea that the monster was called Frankenstein, though this mix-up was already in effect in the preceding decades.
As with Frankenstein, Dracula is best known today through movies (take your pick: Bela Lugosi, Christopher Lee, Gary Oldman, etc.) and other forms of popular culture rather than the original novel.
The success of the The Lord of the Rings films has dramatically colored public perception of the work, for better or worse, since the films put their own dramatically different spin on various themes. The number of people who read the books for the first time prior to seeing the films or knowing everything that happens therein is expected to approach zero. The studio struggled for a while to get the prequel, The Hobbit, off the ground, due in part to the pressure of making it conform to the existing films (and turning it into a trilogy).
It seemed that the 2004 adaptation of Catwoman starring Halle Berry would kill any chance for a reasonable adaptation for quite some time... though the character appears in The Dark Knight Rises, played by Anne Hathaway. (Notably, this version of Selina Kyle doesn't wear the iconic outfit and is not even called Catwoman — possibly because of this stigma.)
Averted with Popeye. This 1980 Robert Altman adaptation, with Robin Williams as the world-famous sailor man, notoriously tried to recreate the 10-minute cartoon format at feature length and failed miserably. Most critics and audiences, many of whom were unfamiliar with the original source material, were so disgusted with the movie that the Max Fleischer cartoons looked much, much better by comparison. Those cartoons continued to be popular on TV long after the movie was forgotten.
For most people, Superman is synonymous with the Christopher Reeve movies, to the point that many critics of Man of Steel were off-put by the fact that it wasn't as light and tame as the Reeve films.
The failure of Disney's quarter-billion-dollar 2012 John Carter has killed any further attempts to bring Edgar Rice Burroughs' other hero to the big or small screen by Disney or anyone else for at least a few decades.
The King James version of The Bible, with its antiquated (it was deliberately a bit archaic even in James' day) version of English, seems to have produced in some people the rather bizarre notion that God speaks Ye Olde Englishe exclusively, and that it's very nearly sacrilegious to use modern English when speaking to or about Him. To this day, there are a great many Christians and Christian denominations (especially those on the fundamentalist end), known as "King James Onlyites", who will insist that the King James Version is the only English translation "approved" by God, and can get very touchy on the subject. However, these people are in the minority in much of the world. This is especially ironic/silly when you consider just why people like the KJV: Because it is the version of the Bible with the most artistic merit; rather than just a translation of the Hebrew, it is a work of English verse in its own right. In other words, it isn't a literal translation.
The later runs of The Princess Bride include post-novel content in which Goldman tells us (Kayfabe) that Stephen King felt this way about Goldman's abridged version of the story.
The re-imagined Battlestar Galactica had to deal with the cheesy legacy of its predecessor. True, the original did have a lot of fans but even a larger segment who only remembered the funny costumes, the IN SPACE! plots and, oh gods, the kids... The new show's success and the ire it drew from the fans of the original was a result of its efforts to distance itself from these aspects by going Darker and Edgier. One of Ronald D. Moore's main aims in re-imagining the BSG was to "take from the old show what worked and leave the rest" and he genuinely seemed to believe that the original show had a very good premise that simply could not be portrayed justly in the 1970s.
The 70s Wonder Woman series starring Lynda Carter colored, and continues to color, peoples' cultural knowledge of the character. Unlike Batman, however, Wonder Woman has never had the benefit of a successive adaptation that mitigates the Camp elements of the 70s show. The Justice League animated series has helped to some extent, but popular culture still looks almost exclusively to the Carter version, and a recent adaptation with Adrianne Palicki was cancelled before it aired. And because, unlike the Batman show, it very rarely attempted to adapt any of the villain concepts from the comics (and one of the only ones they did take from the comics was of a character who underwent a fairly quick full redemption arc, not even with a final sacrificial death or anything), it's also left future generations of cinematic talent (directors, writers and producers) floundering to find a villain from the comics that the mainstream will care about. In that sense, the Wonder Woman show that made it to air is probably a FAR worse blow to her than the Adam West Batman was to Batman. In fact, let's say we put up a plausible epitaph: "Here rests the hopes of a good and ageless piece of media focused on a female superhero. The producers were too lazy to search for a superheroine that had a Rogues Gallery they were actually interested in. R.I.P. 1941-1975." Until one comes along, that's the current last word.
While Power Rangers is a successful franchise on its own, many Super Sentai purists view it as the reason why Super Sentai will never get the proper international recognition it deserves, since the adapted footage of the costumes and giant robot battles are so deeply ingrained with Power Rangers, Super Sentai could never stand on its own merits. It's not uncommon to see Super Sentai videos on the internet (such as the "Legendary War" scene from Kaizoku Sentai Gokaiger) to be labeled as Power Rangers videos. This is especially prevalent among fans from countries such as Brazil, the Philippines, or France, which used to air locally-dubbed versions of Super Sentai before switching to Power Rangers dubs.
On another level, the individual Sentai seasons can be tarred with the Rangers brush. Some past seasons get a bad reputation simply because of the following Rangers adaptations. Some fans who watch Rangers first looked a little skeptically on Gaoranger or Boukenger simply because of how badly they were adapted into Wild Force or Operation Overdrive.
This also applies to tokusatsu in general. Fairly often people would call any costumed superhero from Japan "a Power Ranger", despite having no resemblance to one whatsoever.
The 60s TV interpretation of Batman with its campy costumes, ludicrous gadgets and cheesy Hit Flash effects still linger on as some people's view of the character, despite several adaptations and major character changes since. This has continued to the extent that Warner Bros. Consumer Products has approached Adam West and 20th Century Fox (producers of the TV show) in 2012 about producing merchandise based on the TV shows. (Also, greeting cards from Hallmark tend to follow the Adam West design, which most closely resembled the traditional comic book design.) The Jim Holmes incident may further encourage this revival of the West version.
The TV series was a distillation of the very worst of The Comics Code/Silver Age era Batman comics, roughly late '50s to mid '60s. In fact some say that the later (1970s-80s) portrayals of Batman were a backlash against the show. In Amazing Heroes#119 in 1987 (two years before the Michael Keaton film), Max Allan Collins had an interview. He said the following:
“I’m afraid what I’m running smack up into is the old Batman TV show controversy: the old business about, Gee that was a TV show that made fun of Batman and made fun of comic books, so we have to show people that Batman and comic books are serious and they’re adult and accordingly all the fun goes out of it. There was a reason why that TV show was played for laughs and that is when you put actual human beings in those costumes and act out those stories, it looks stupid. They betray their juvenile roots. It can’t be done straight. I defy them to do the movie straight”.
In some ways, Batman was an ink stain for the genre of Western superheroes. Until 2000 or so, when superhero movies started being huge, any outside journalism on the genre would feature "Bif! Pow!" in the headline, as if Adam West was the last word on the subject.
Due to mostly adapting villains who actually appeared in the comics, it still managed to give the mainstream SOME SORT of sense of who was supposed to be the big and popular villains, so (even if you don't like it) it can be said to be a sort of useful failure. Unlike the Lynda Carter Wonder Woman show, which adapted pretty much none of them.
Masked Rider, Saban's adaptation of Kamen Rider Black RX, was not just an ink stain to the Kamen Rider franchise itself, it was also an ink stain to its very own name. Originally "Masked Rider" was the official romanized name of Kamen Rider (kamen simply means "mask" in Japanese), but because the name "Masked Rider" is so closely associated to the Saban version outside Japan, most fans refuse to use it despite its prominence in many products. When Adness made Kamen Rider Dragon Knight (a remake of Kamen Rider Ryuki), Executive Producer Steve Wang insisted on using "Kamen Rider" instead of "Masked Rider" since he wanted to distance the show from the Saban version. The Japanese shows, which were using the romanized name of "Masked Rider" on the logos since Kamen Rider Kuuga, followed suit by switching to "Kamen Rider" beginning with Kamen Rider Double. On top of that, some time ago Saban applied for a trademark for "Power Rider", which many believe is their giving "Kamen Rider" another swing.
Although the book series it was based off of was reasonably popular at the time, the Dinotopia miniseries has colored the view of the entire franchise in the minds of many.
Bloody Roar: Each sequel after the 2nd further destroyed people's perceptions that the game involved any skill or strategy, culminating with Bloody Roar 4, where one could almost justly assume the entire series was just a Button Masher.
ToeJam & Earl had many Rogue Lite elements about 20 years before the term "Rogue Lite" came into common use, and had many aspects that were rarely seen in console games, but a glance at its good but less creative side-scrolling sequel or the unimpressive third game can make a casual observer overlook the original.
Super Friends has crippled Aquaman as a character forever. Give him a harpoon hand, replace it with a magical water hand, point out how life at the bottom of the ocean has made him stronger, faster, and more resilient than most humans... and everyone will still be like, "He's just some guy who swims fast and talks to fish." It's gotten to the point where DC finally decided to kill off the old Aquaman and create a new one.
But the original is back now, and in New 52, all bets and gloves are off with DC, as they hire expert comic book fixer Geoff Johns to fix Aquaman's bad cred. As Geoff has had Aquaman face all of the 'fish man' jokes and blow them to shreds with all of the awesome things he does, it seems to be working.
Hawkman, too, lost a great deal of what made him great. Among companions who could fly and bench-press planets, or fly and become living lightning, or fly and create any green-colored thing they could imagine, Hawkman was the Super Friend who could fly ... and do nothing else.
Everyone remembers the 1987 Teenage Mutant Ninja Turtles cartoon, while the much darker original comics and more recent cartoon and movies seem to be living in its shadow... Much like the '60s Batman example earlier in the page.
Everyone remembers He-Man and the Masters of the Universe (1983), with its goofy takes on the characters and the moral segments at the end. Very few remember the previous DC Comics take on Masters of the Universe, where the Sorceress is referred to as 'The Goddess' and lives in a cave (and not Castle Greyskull—and she and Zoar the falcon are separate characters), Prince Adam (He-Man's alter-ego who didn't appear in the toyline minicomics... at first) is known for 'wenching and carousing', and Skeletor is a much more dangerous villain who kills a rival wizard in combat. There were also illustrated books released with the original action figures which gave different origins for the characters (Teela, instead of being the Sorceress' daughter, is a magical clone of hernote which practically makes Teela her "daughter" anyway), and had a storyline where He-Man's Sword of Power was split in two (with He-Man possessing one half and Skeletor the other—this was reflected in the original action figure accessories with two 'sword halves' with the characters' figures that could be put together). Later takes on He-Man and the Masters of the Universe (such as the 1987 live-action movie and the 2002 series) don't seem to be talked about as much as the 80's Filmation cartoon.
A rare positive example is the effect that the episode "Heart Of Ice" had on the character of Mr. Freeze in Batman: The Animated Series. The episode had given him a tearjerking backstory and a beautifully done characterization that is considered canon by comics and fans, overriding his relatively flat '60s version.
When people think of Aladdin, odds are they'll think of the Disney version with its storybook version of Persia/Arabia, rather than the Chinese setting that the original story employed. To be fair, nearly all adaptations of Aladdin were set in Arabia well before Disney got their hands on the story.
Pocahontas, meanwhile, is one of the biggest subversions. The legend of John Smith and Pocahontas being lovers had built for centuries—but once Disney put that myth to celluloid, the Vocal Minority that knew its inaccuracies raised such a stink that everyone now knows the real Pocahontas was only twelve years old at the time and Smith probably didn't even care that she existed. She even married John Rolfe and moved with him to England, a fact that Disney inexplicably got right in the direct-to-video sequel.
Inverted in the case of The Real Ghostbusters and Ghostbusters 2. It's been said GB2 is seen as the runt of the franchise because RGB set such a high standard with writing and characterization.